Comprehensive genotyping of the USA national maize inbred seed bank

Abstract

BackgroundGenotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world.ResultsThe method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits.ConclusionsThe genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.

Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits

“…This could be illustrated, for instance, by the discovery by Romay et al (2013) of a single SNP within the ZmCCT region highly associated with the flowering time gene among 680 000 SNPs. Increasing the number of markers would be of great value for a more in-depth analysis of this Differential power in association mapping of 24 maize phenology and plant architecture traits S Bouchet et al data set but the density that was used in this study nevertheless gave some general and specific information about the genetic architecture of most traits.…”

“…However, substantial variation remains to be explained and exploited for most traits. QTL mapping experiments revealed that plant total height (PTHT) and flowering time are highly heritable polygenic traits and that their variation is controlled by many unlinked genes, each contributing a small additive effect (Buckler et al, 2009;Romay et al, 2013;Bouchet et al, 2013;Peiffer et al, 2014). Many QTL experiments for inflorescence traits showed that they are less heritable (Brown et al, 2011).…”

“…Association studies on diversity panels are effective for identifying genetic variants associated with phenological and morphological traits in maize (Thornsberry et al, 2001;Flint-Garcia et al, 2005;CamusKulandaivelu et al, 2006;Ducrocq et al, 2008Ducrocq et al, , 2009Durand et al, 2012;Romay et al, 2013;Bouchet et al, 2013). In the current study, 375 lines of maize originating from the tropics, USA and Europe were successfully phenotyped for 24 ecologically and agronomically important traits related to (i) phenology, (ii) plant architecture, (iii) ear and yield components and (iv) tassel architecture.…”

Plant genomics: sowing the seeds of success

“…To address this, Romay et al [7] perform genotyping-by-sequencing of 681,257 SNP markers in the 2,815 maize accessions in the USA national maize inbred seed bank. This resource will be invaluable for the analysis of genetic diversity within the publicly available maize panel using genome-wide association studies and genomic selection approaches.…”

Prediction of Hybrid Performance in Crop Plants: Molecular and Recent Approaches

“…Even if completed reference sequence of the plant species is not available, the reducedrepresentation genotyping-by sequencing (GBS) methods enable use of NGS technologies for high-throughput genomic resequencing, at a constantly shrinking price. Romay et al, (2013) generate almost 7lacs genome wide SNPs in a panel of 2815 diverse inbred lines. Further, assemblies of crop relative genome diversity provide pangenome which gives unprecedented insight into the gene diversity available in secondary crop gene pools Lu et al, (2015).…”